Nucleotide sequences encoding fasciated ear3 (fea3) and methods of use thereof

ABSTRACT

Methods and compositions for modulating shoot apical meristem size are provided. Methods are provided for modulating the expression of fea3 sequence in a host plant or plant cell to modulate agronomic characteristics such as altered size and number of organs, including plant seeds.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 61/610,645, filed Mar. 14, 2012, and U.S. Provisional Application No. 61/751,326, filed Jan. 11, 2013, the entire content of each is herein incorporated by reference.

FIELD OF THE INVENTION

The invention relates to the field of the genetic manipulation of plants, particularly the modulation of gene activity and development in plants.

BACKGROUND OF THE INVENTION

Leaves and the axillary meristems that generate branches and flowers are initiated in regular patterns from the shoot apical meristem (SAM). The cells of the shoot apical meristem summit serve as stem cells that divide to continuously displace daughter cells to the surrounding regions, where they are incorporated into differentiated leaf or flower primordia. The meristems are thus capable of regulating their size during development by balancing cell proliferation with the incorporation of cells into new primordia. The SAM provides all aerial parts of plant body. The central concept of stem cells regulation is known by the signal pathway of CLAVATA/WUSCHEL (CLV/WUS) genes. Loss of CLV1, CLV2, or CLV3 activity in Arabidopsis causes accumulation of undifferentiated cells in the shoot apex, indicating that CLV genes together promote the timely transition of stem cells into differentiation pathways, or repress stem cell division, or both (Fletcher et al. (1999) Science 283:1911-1914; Taguchi-Shiobara et al. (2001) Genes and Development 15:2755-5766; Trotochaud et al. (1999) Plant Cell 11:393-405; Merton et al. (1954) Am. J. Bot. 41:726-32; Szymkowiak et al. (1992) Plant Cell 4:1089-100; Yamamoto et al. (2000) Biochim. Biophys. Acta. 1491:333-40). The maize orthologue of CLV1 is TD1 (Bommert et al. (2005) Development 132:1235-1245). The maize orthologue of CLV2 is FEA2 (Taguchi-Shiobara et al. (2001) Genes Dev. 65 15:2755-2766). It is desirable to be able to control the size and appearance of shoot and floral meristems, to give increased yields of leaves, flowers, and fruit. Accordingly, it is an object of the invention to provide novel methods and compositions for the modulation of meristem development.

SUMMARY OF THE INVENTION

In one embodiment, the current invention provides a method of producing a transgenic plant with decreased expression of endogenous fea3, the method comprising the steps of (a) introducing into a regenerable plant cell a recombinant construct comprising a polynucleotide sequence operably linked to a promoter, wherein the expression of the polynucleotide sequence reduces endogenous fea3 expression; (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and (c) selecting a transgenic plant of (b), wherein the transgenic plant comprises the recombinant DNA construct and exhibits a decrease in expression of fea3, when compared to a control plant not comprising the recombinant DNA construct.

In another embodiment, the current invention provides a method of producing a transgenic plant with decreased expression of endogenous fea3, the method comprising the steps of (a) introducing into a regenerable plant cell a recombinant DNA construct comprising an isolated polynucleotide operably linked, in sense or antisense orientation, to a promoter functional in a plant, wherein the polynucleotide comprises: (i) the nucleotide sequence of SEQ ID NO:1, 2 or 4; (ii) a nucleotide sequence with at least 90% sequence identity, based on the Clustal W method of alignment, when compared to SEQ ID NO:1, 2 or 4; (iii) a nucleotide sequence of at least 100 contiguous nucleotides of SEQ ID NO:1, 2 or 4; (iv) a nucleotide sequence that can hybridize under stringent conditions with the nucleotide sequence of (i); or (v) a modified plant miRNA precursor, wherein the precursor has been modified to replace the miRNA encoding region with a sequence designed to produce a miRNA directed to SEQ ID NO:1, 2 or 4; (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and (c) selecting a transgenic plant of (b), wherein the transgenic plant comprises the recombinant DNA construct and exhibits a decrease in expression of fea3, when compared to a control plant not comprising the recombinant DNA construct.

One embodiment of the invention is a method of producing a transgenic plant with alteration of an agronomic characteristic, the method comprising the steps of (a) introducing into a regenerable plant cell a recombinant DNA construct comprising an isolated polynucleotide operably linked to at least one regulatory sequence, wherein the polynucleotide encodes a fragment or a variant of a polypeptide having an amino acid sequence of at least 80% sequence identity, based on the Clustal W method of alignment, when compared to SEQ ID NO:3 or 5, wherein the fragment or the variant confers a dominant-negative phenotype in the regenerable plant cell; (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and (c) selecting a transgenic plant of (b), wherein the transgenic plant comprises the recombinant DNA construct and exhibits an alteration of at least one agronomic characteristic selected from the group consisting of: ear meristem size, kernel row number, leaf number, inflorescence number, branching within the inflorescence, flower number, fruit number, seed number, root branching, root biomass, root lodging, biomass and yield, when compared to a control plant not comprising the recombinant DNA construct.

Another embodiment of the current invention is the above method wherein expression of the polypeptide of part (a) in a plant line having the fea3 mutant genotype is capable of partially or fully restoring the wild-type phenotype.

One embodiment of the current invention is a method of identifying a weaker allele of fea3, the method comprising the steps of (a) performing a genetic screen on a population of mutant maize plants (b) identifying one or more mutant maize plants that exhibit weak fea3 phenotype than a fea3 null plant; and (c) identifying the weak fea3 allele from the mutant maize plant with weaker fea3 phenotype.

One embodiment of the current invention is a method of identifying a weaker allele of fea3, the method comprising the steps of: (a) gene shuffling using SEQ ID NOS:1, 2 or 4; (b) transforming the shuffled sequences from step (a) into a population of regenerable plant cells; (c) regenerating a population of transformed plants from the population of transformed regenerable plant cells of step (b); (d) screening the population of transformed plants from step (c) for weak fea3 phenotype; and (e) identifying the weak fea3 allele from the transformed plant exhibiting weak fea3 phenotype.

One embodiment of the invention is a plant in which expression of the endogenous fea3 gene is inhibited relative to a control plant. Another embodiment of the current invention is a method of making said plant, the method comprising the steps of (a) introducing a mutation into the endogenous fea3 gene; and (b) detecting the mutation, wherein the mutation is effective in inhibiting the expression of the endogenous fea3 gene. In one embodiment, the steps (a) and (b) are done using Targeting Induced Local Lesions IN Genomics (TILLING) method. In embodiment, the mutation is a site-specific mutation.

One embodiment of the invention is a plant that exhibits weaker fea3 phenotype relative to a wild-type plant. Another embodiment is a method of making said plant wherein the method comprises the steps of: (a) introducing a transposon into a germ plasm containing an endogenous fea3 gene; (b) obtaining progeny of the germplasm of step (a); (c) and identifying a plant of the progeny of step (b) in which the transposon has inserted into the endogenous FEA3 gene and a reduction of expression of fea3 is observed. Step (a) may further comprise introduction of the transposon into a regenerable plant cell of the germ plasm by transformation and regeneration of a transgenic plant from the regenerable plant cell, wherein the transgenic plant comprises in its genome the transposon.

In one embodiment, the methods described above wherein the method further comprises the steps of (a) introducing into a regenerable plant cell a recombinant construct comprising the weak fea3 allele identified by the methods described above; (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and (c) selecting a transgenic plant of (b), wherein the transgenic plant comprises the recombinant DNA construct and exhibits a weak fea3 phenotype, when compared to a control plant not comprising the recombinant DNA construct.

Another embodiment is a method of producing a transgenic plant with an alteration in agronomic characteristic, the method comprising (a) introducing into a regenerable plant cell a recombinant DNA construct comprising an isolated polynucleotide operably linked, in sense or antisense orientation, to a promoter functional in a plant, wherein the polynucleotide comprises: (i) the nucleotide sequence of SEQ ID NO:1, 2 or 4; (ii) a nucleotide sequence with at least 90% sequence identity, based on the Clustal W method of alignment, when compared to SEQ ID NO:1, 2 or 4; (iii) a nucleotide sequence of at least 100 contiguous nucleotides of SEQ ID NO:1, 2 or 4; (iv) a nucleotide sequence that can hybridize under stringent conditions with the nucleotide sequence of (i); or (v) a modified plant miRNA precursor, wherein the precursor has been modified to replace the miRNA encoding region with a sequence designed to produce a miRNA directed to SEQ ID NO:1, 2 or 4; (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and (c) selecting a transgenic plant of (b), wherein the transgenic plant comprises the recombinant DNA construct and exhibits an alteration in at least one agronomic characteristic selected from the group consisting of: enlarged ear meristem, kernel row number, seed number, root branching, root biomass, root lodging, biomass and yield, when compared to a control plant not comprising the recombinant DNA construct. Another embodiment is the plant produced by this method.

One embodiment is a method of expressing a heterologous polynucleotide in a plant, the method comprising (a) transforming a regenerable plant cell with a recombinant DNA construct comprising a heterologous polynucleotide operably linked to a second polynucleotide, wherein the second polynucleotide is a FEA3 promoter (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and (c) selecting a transgenic plant of (b), wherein the transgenic plant comprises the recombinant DNA construct and further wherein the heterologous polynucleotide is expressed in the transgenic plant. Another embodiment is the plant comprising in its genome a recombinant DNA construct comprising a heterologous polynucleotide operably linked to a second polynucleotide, wherein the second polynucleotide is a FEA3 promoter and wherein the heterologous polynucleotide is expressed in the plant.

Another embodiment is a method of identifying a first maize plant or a first maize germplasm that has an alteration of at least one agronomic characteristic, the method comprising detecting in the first maize plant or the first maize germplasm at least one polymorphism of a marker locus that is associated with said phenotype, wherein the marker locus encodes a polypeptide comprising an amino acid sequence selected from the group consisting of: a) an amino acid sequence having at least 90% and less than 100% sequence identity to SEQ ID NO:3 or 5, wherein expression of said polypeptide in a plant or plant part thereof results in an alteration of at least one agronomic characteristic selected from the group consisting of: ear meristem size, kernel row number, inflorescence number, branching within the inflorescence, flower number, fruit number, and seed number, when compared to a control plant, wherein the control plant comprises SEQ ID NO:3 or 5. Another embodiment is the above method wherein said polypeptide comprises the sequence set forth in SEQ ID NO:23, 25 or 27.

The invention includes a recombinant DNA construct comprising an isolated polynucleotide of the current invention operably linked, in sense or antisense orientation, to a promoter that is shoot apical meristem specific or shoot apical meristem preferred.

This invention includes a vector, cell, plant, or seed comprising any of the recombinant DNA constructs described in the present invention.

The invention encompasses plants produced by the methods described herein.

The invention also encompasses regenerated, mature and fertile transgenic plants comprising the recombinant DNA constructs described above, transgenic seeds produced therefrom, T1 and subsequent generations. The transgenic plant cells, tissues, plants, and seeds may comprise at least one recombinant DNA construct of interest.

In one embodiment, the plant is selected from the group consisting of: Arabidopsis, tomato, maize, soybean, sunflower, sorghum, canola, wheat, alfalfa, cotton, rice, barley, millet, sugar cane and switchgrass.

In one embodiment, the plant comprising the recombinant constructs described in the present invention is a monocotyledonous plant. In another embodiment, the plant comprising the recombinant constructs described in the present invention is a maize plant.

BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE LISTINGS

The invention can be more fully understood from the following detailed description and the accompanying drawings and Sequence Listing which form a part of this application. The Sequence Listing contains the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IUBMB standards described in Nucleic Acids Research 13:3021-3030 (1985) and in the Biochemical Journal 219 (No. 2): 345-373 (1984), which are herein incorporated by reference in their entirety. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. § 1.822.

FIG. 1 shows the map-based cloning approach used to isolate the fea3-Reference allele.

FIG. 2A shows RT-PCR data showing the expression analysis of fea2 and fea3 in different tissues. The different tissues analyzed are RAM: root apical meristem; RE: root elongation zone; RAM(I): RAM of lateral root; SAM; shoot apical meristem (including leaf primordia); EM: ear inflorescence meristem FIG. 2B shows fea3 expression in situ. FIG. 2C shows western blot with anti-RFP antibody of RFP-tagged FEA3, of membrane fractionated samples from non-transgenic WT and transgenic plants expressing RFP tagged FEA3 protein. “T” is the “total, unfractionated sample”, “S” is the soluble fraction and “M” is the membrane fraction.

FIG. 3B-3E shows the fasciated fea3 phenotype in ear development compared to that in a wild-type (wt) plant (FIG. 3A).

FIG. 4A-4C show the phenotypic analysis of fea3/fea2 double mutants.

FIG. 4A shows the comparison between the tassels of double mutants compared to single mutants and wt plants. FIG. 4B shows the spikelet density comparison between double mutants, single mutants and wt plants. FIG. 4C shows a comparison between double mutant ear phenotypes compared to single mutants and wt plants.

FIG. 5A and FIG. 5B shows a comparison between wt plants, fea2 and fea3 plants in the CLV3 peptide root assay. FIG. 5B shows the quantitative analysis.

FIG. 6 shows a quantitative analysis of the comparison between wt plants, fea2 and fea3 plants in the CLV3-like peptide root assay.

FIG. 7A and FIG. 7B shows wt and fea3 embryos cultured in the presence of FCP1 and scrambled peptide. FIG. 7A shows wt and fea3 embryo SAM growth, and

FIG. 7B shows a quantitative analysis of the same.

FIG. 8A-8C show the phenotypic analysis of fea3/td1 double mutants.

The sequence descriptions (Table 1) and Sequence Listing attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. § 1.821-1.825. The Sequence Listing contains the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IUBMB standards described in Nucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical J. 219 (2):345-373 (1984) which are herein incorporated by reference. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. § 1.822.

SEQ ID NO:1 is the nucleotide sequence of the fea3 wt gene.

SEQ ID NO:2 is the coding sequence of wt fea3.

SEQ ID NO:3 is the amino acid sequence of wt fea3.

SEQ ID NO:4 is the coding sequence of alternatively spliced shorter fea3.

SEQ ID NO:5 is the amino acid sequence of alternatively spliced shorter fea3.

SEQ ID NO:6 is the amino acid sequence encoded by the nucleotide sequence corresponding to the locus At1g68780 (Arabidopsis thaliana).

SEQ ID NO:7 is the amino acid sequence encoded by the nucleotide sequence corresponding to the locus At1g13230 (Arabidopsis thaliana).

SEQ ID NO:8 is the amino acid sequence encoded by the nucleotide sequence corresponding to the locus At3g25670 (Arabidopsis thaliana).

SEQ ID NO:9 is the amino acid sequence corresponding to the locus LOC_Os05g43140.1, a rice (japonica) predicted protein from the Michigan State University Rice Genome Annotation Project Osa1 release 6 (January 2009).

SEQ ID NO:10 is the amino acid sequence corresponding to Sb03g008380, a sorghum (Sorghum bicolor) predicted protein from the Sorghum JGI genomic sequence version 1.4 from the US Department of energy Joint Genome Institute.

SEQ ID NO:11 is the amino acid sequence corresponding to Sb03g008360, a sorghum (Sorghum bicolor) predicted protein from the Sorghum JGI genomic sequence version 1.4 from the US Department of energy Joint Genome Institute.

SEQ ID NO:12 is the amino acid sequence corresponding to Glyma20g32610, a soybean (Glycine max) predicted protein from predicted coding sequences from Soybean JGI Glyma1.01 genomic sequence from the US Department of energy Joint Genome Institute.

SEQ ID NO:13 is the amino acid sequence corresponding to Glyma10g34950, a soybean (Glycine max) predicted protein from predicted coding sequences from Soybean JGI Glyma1.01 genomic sequence from the US Department of energy Joint Genome Institute.

SEQ ID NO:14 is the amino acid sequence corresponding to Glyma02g11350, a soybean (Glycine max) predicted protein from predicted coding sequences from Soybean JGI Glyma1.01 genomic sequence from the US Department of energy Joint Genome Institute.

SEQ ID NO:15 is the amino acid sequence corresponding to Glyma01g22730, a soybean (Glycine max) predicted protein from predicted coding sequences from Soybean JGI Glyma1.01 genomic sequence from the US Department of energy Joint Genome Institute.

SEQ ID NO:16 is the amino acid sequence corresponding to Glyma05g07800, a soybean (Glycine max) predicted protein from predicted coding sequences from Soybean JGI Glyma1.01 genomic sequence from the US Department of energy Joint Genome Institute.

SEQ ID NO:17 is the amino acid sequence corresponding to Glyma17g13210, a soybean (Glycine max) predicted protein from predicted coding sequences from Soybean JGI Glyma1.01 genomic sequence from the US Department of energy Joint Genome Institute.

SEQ ID NO:18 is the nucleotide sequence of a fea3 homolog from Ascelpias syriaca.

SEQ ID NO:19 is the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO:18.

SEQ ID NO:20 is the nucleotide sequence of fea3-0 reference allele.

SEQ ID NO:21 is the protein sequence of fea3-0 reference allele, encoded by SEQ ID NO:20.

SEQ ID NO:22 is the nucleotide sequence of the EMS mutant fea3-1.

SEQ ID NO:23 is the protein sequence of the EMS mutant allele fea3-1, encoded by the nucleotide sequence given in SEQ ID NO:22.

SEQ ID NO:24 is the nucleotide sequence of the EMS mutant fea3-2.

SEQ ID NO:25 is the protein sequence of the EMS mutant allele fea3-2, encoded by the nucleotide sequence given in SEQ ID NO:24.

SEQ ID NO:26 is the nucleotide sequence of the EMS mutant fea3-3.

SEQ ID NO:27 is the protein sequence of the EMS mutant allele fea3-3, encoded by the nucleotide sequence given in SEQ ID NO:26.

SEQ ID NO:28 is the nucleotide sequence of the FEA3 promoter.

SEQ ID NO:29 is the nucleotide sequence encoding the signal peptide of the FEA3 protein.

SEQ ID NO:30 is the nucleotide sequence encoding the RFP-FEA3 fusion protein.

SEQ ID NO:31 is the nucleotide sequence of the FEA3 3′-UTR.

SEQ ID NOS:32-38 are the sequences of the peptides (ZCL3, FCP1, CLV3, CLE20, CLE40, ZCL21 and ZCL23 respectively) used for the CLV3/CLV3-like peptide assay described in Example 10.

The sequence descriptions and Sequence Listing attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. § 1.821-1.825.

The Sequence Listing contains the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IUBMB standards described in Nucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical J. 219 (No. 2):345-373 (1984) which are herein incorporated by reference. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. § 1.822.

DETAILED DESCRIPTION OF THE INVENTION

The disclosure of each reference set forth herein is hereby incorporated by reference in its entirety.

As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a plant” includes a plurality of such plants, reference to “a cell” includes one or more cells and equivalents thereof known to those skilled in the art, and so forth.

As used herein:

The terms “monocot” and “monocotyledonous plant” are used interchangeably herein. A monocot of the current invention includes the Gramineae.

The terms “dicot” and “dicotyledonous plant” are used interchangeably herein. A dicot of the current invention includes the following families: Brassicaceae, Leguminosae, and Solanaceae.

The terms “full complement” and “full-length complement” are used interchangeably herein, and refer to a complement of a given nucleotide sequence, wherein the complement and the nucleotide sequence consist of the same number of nucleotides and are 100% complementary.

“Transgenic” refers to any cell, cell line, callus, tissue, plant part or plant, the genome of which has been altered by the presence of a heterologous nucleic acid, such as a recombinant DNA construct, including those initial transgenic events as well as those created by sexual crosses or asexual propagation from the initial transgenic event. The term “transgenic” as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.

“Genome” as it applies to plant cells encompasses not only chromosomal DNA found within the nucleus, but organelle DNA found within subcellular components (e.g., mitochondrial, plastid) of the cell.

“Plant” includes reference to whole plants, plant organs, plant tissues, seeds and plant cells and progeny of same. Plant cells include, without limitation, cells from seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores.

“Progeny” comprises any subsequent generation of a plant.

“Transgenic plant” includes reference to a plant which comprises within its genome a heterologous polynucleotide. For example, the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The heterologous polynucleotide may be integrated into the genome alone or as part of a recombinant DNA construct.

A “trait” refers to a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell. In some instances, this characteristic is visible to the human eye, such as seed or plant size, or can be measured by biochemical techniques, such as detecting the protein, starch, or oil content of seed or leaves, or by observation of a metabolic or physiological process, e.g. by measuring tolerance to water deprivation or particular salt or sugar concentrations, or by the observation of the expression level of a gene or genes, or by agricultural observations such as osmotic stress tolerance or yield.

“Agronomic characteristic” is a measurable parameter including but not limited to, ear meristem size, tassel size, greenness, yield, growth rate, biomass, fresh weight at maturation, dry weight at maturation, fruit yield, seed yield, total plant nitrogen content, fruit nitrogen content, seed nitrogen content, nitrogen content in a vegetative tissue, total plant free amino acid content, fruit free amino acid content, seed free amino acid content, free amino acid content in a vegetative tissue, total plant protein content, fruit protein content, seed protein content, protein content in a vegetative tissue, drought tolerance, nitrogen uptake, root branching, root biomass, root lodging, harvest index, stalk lodging, plant height, ear height, ear length, salt tolerance, early seedling vigor and seedling emergence under low temperature stress.

“Heterologous” with respect to sequence means a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.

“Polynucleotide”, “nucleic acid sequence”, “nucleotide sequence”, or “nucleic acid fragment” are used interchangeably to refer to a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. Nucleotides (usually found in their 5′-monophosphate form) are referred to by their single letter designation as follows: “A” for adenylate or deoxyadenylate (for RNA or DNA, respectively), “C” for cytidylate or deoxycytidylate, “G” for guanylate or deoxyguanylate, “U” for uridylate, “T” for deoxythymidylate, “R” for purines (A or G), “Y” for pyrimidines (C or T), “K” for G or T, “H” for A or C or T, “I” for inosine, and “N” for any nucleotide.

“Polypeptide”, “peptide”, “amino acid sequence” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. The terms “polypeptide”, “peptide”, “amino acid sequence”, and “protein” are also inclusive of modifications including, but not limited to, glycosylation, lipid attachment, sulfation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation.

“Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into protein by the cell.

“cDNA” refers to a DNA that is complementary to and synthesized from an mRNA template using the enzyme reverse transcriptase. The cDNA can be single-stranded or converted into the double-stranded form using the Klenow fragment of DNA polymerase I.

“Coding region” refers to a polynucleotide sequence that when transcribed, processed, and/or translated results in the production of a polypeptide sequence.

An “Expressed Sequence Tag” (“EST”) is a DNA sequence derived from a cDNA library and therefore is a sequence which has been transcribed. An EST is typically obtained by a single sequencing pass of a cDNA insert. The sequence of an entire cDNA insert is termed the “Full-Insert Sequence” (“FIS”). A “Contig” sequence is a sequence assembled from two or more sequences that can be selected from, but not limited to, the group consisting of an EST, FIS and PCR sequence. A sequence encoding an entire or functional protein is termed a “Complete Gene Sequence” (“CGS”) and can be derived from an FIS or a contig.

“Mature” protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or pro-peptides present in the primary translation product have been removed.

“Precursor” protein refers to the primary product of translation of mRNA; i.e., with pre- and pro-peptides still present. Pre- and pro-peptides may be and are not limited to intracellular localization signals.

“Isolated” refers to materials, such as nucleic acid molecules and/or proteins, which are substantially free or otherwise removed from components that normally accompany or interact with the materials in a naturally occurring environment. Isolated polynucleotides may be purified from a host cell in which they naturally occur. Conventional nucleic acid purification methods known to skilled artisans may be used to obtain isolated polynucleotides. The term also embraces recombinant polynucleotides and chemically synthesized polynucleotides.

“Recombinant” refers to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques. “Recombinant” also includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid or a cell derived from a cell so modified, but does not encompass the alteration of the cell or vector by naturally occurring events (e.g., spontaneous mutation, natural transformation/transduction/transposition) such as those occurring without deliberate human intervention.

“Recombinant DNA construct” refers to a combination of nucleic acid fragments that are not normally found together in nature. Accordingly, a recombinant DNA construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that normally found in nature.

The terms “entry clone” and “entry vector” are used interchangeably herein.

“Regulatory sequences” or “regulatory elements” are used interchangeably and refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include, but are not limited to, promoters, translation leader sequences, introns, and polyadenylation recognition sequences. The terms “regulatory sequence” and “regulatory element” are used interchangeably herein.

“Promoter” refers to a nucleic acid fragment capable of controlling transcription of another nucleic acid fragment.

“Promoter functional in a plant” is a promoter capable of controlling transcription in plant cells whether or not its origin is from a plant cell.

“Tissue-specific promoter” and “tissue-preferred promoter” are used interchangeably to refer to a promoter that is expressed predominantly but not necessarily exclusively in one tissue or organ, but that may also be expressed in one specific cell.

“Developmentally regulated promoter” refers to a promoter whose activity is determined by developmental events.

“Operably linked” refers to the association of nucleic acid fragments in a single fragment so that the function of one is regulated by the other. For example, a promoter is operably linked with a nucleic acid fragment when it is capable of regulating the transcription of that nucleic acid fragment.

“Expression” refers to the production of a functional product. For example, expression of a nucleic acid fragment may refer to transcription of the nucleic acid fragment (e.g., transcription resulting in mRNA or functional RNA) and/or translation of mRNA into a precursor or mature protein.

“Overexpression” refers to the production of a gene product in transgenic organisms that exceeds levels of production in a null segregating (or non-transgenic) organism from the same experiment.

“Phenotype” means the detectable characteristics of a cell or organism.

“Introduced” in the context of inserting a nucleic acid fragment (e.g., a recombinant DNA construct) into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid fragment into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).

A “transformed cell” is any cell into which a nucleic acid fragment (e.g., a recombinant DNA construct) has been introduced.

“Transformation” as used herein refers to both stable transformation and transient transformation.

“Stable transformation” refers to the introduction of a nucleic acid fragment into a genome of a host organism resulting in genetically stable inheritance. Once stably transformed, the nucleic acid fragment is stably integrated in the genome of the host organism and any subsequent generation.

“Transient transformation” refers to the introduction of a nucleic acid fragment into the nucleus, or DNA-containing organelle, of a host organism resulting in gene expression without genetically stable inheritance.

The term “crossed” or “cross” means the fusion of gametes via pollination to produce progeny (e.g., cells, seeds or plants). The term encompasses both sexual crosses (the pollination of one plant by another) and selfing (self-pollination, e.g., when the pollen and ovule are from the same plant). The term “crossing” refers to the act of fusing gametes via pollination to produce progeny.

A “favorable allele” is the allele at a particular locus that confers, or contributes to, a desirable phenotype, e.g., increased cell wall digestibility, or alternatively, is an allele that allows the identification of plants with decreased cell wall digestibility that can be removed from a breeding program or planting (“counterselection”). A favorable allele of a marker is a marker allele that segregates with the favorable phenotype, or alternatively, segregates with the unfavorable plant phenotype, therefore providing the benefit of identifying plants.

The term “introduced” means providing a nucleic acid (e.g., expression construct) or protein into a cell. Introduced includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell, and includes reference to the transient provision of a nucleic acid or protein to the cell. Introduced includes reference to stable or transient transformation methods, as well as sexually crossing. Thus, “introduced” in the context of inserting a nucleic acid fragment (e.g., a recombinant DNA construct/expression construct) into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid fragment into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).

“Suppression DNA construct” is a recombinant DNA construct which when transformed or stably integrated into the genome of the plant, results in “silencing” of a target gene in the plant. The target gene may be endogenous or transgenic to the plant. “Silencing,” as used herein with respect to the target gene, refers generally to the suppression of levels of mRNA or protein/enzyme expressed by the target gene, and/or the level of the enzyme activity or protein functionality. The terms “suppression”, “suppressing” and “silencing”, used interchangeably herein, include lowering, reducing, declining, decreasing, inhibiting, eliminating or preventing. “Silencing” or “gene silencing” does not specify mechanism and is inclusive, and not limited to, anti-sense, cosuppression, viral-suppression, hairpin suppression, stem-loop suppression, RNAi-based approaches, and small RNA-based approaches. Silencing may be targeted to coding regions or non-coding regions, e.g., introns, 5′-UTRs and 3′-UTRs, or both.

A suppression DNA construct may comprise a region derived from a target gene of interest and may comprise all or part of the nucleic acid sequence of the sense strand (or antisense strand) of the target gene of interest. Depending upon the approach to be utilized, the region may be 100% identical or less than 100% identical (e.g., at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical) to all or part of the sense strand (or antisense strand) of the gene of interest.

Suppression DNA constructs are well-known in the art, are readily constructed once the target gene of interest is selected, and include, without limitation, cosuppression constructs, antisense constructs, viral-suppression constructs, hairpin suppression constructs, stem-loop suppression constructs, double-stranded RNA-producing constructs, and more generally, RNAi (RNA interference) constructs and small RNA constructs such as siRNA (short interfering RNA) constructs and miRNA (microRNA) constructs.

“Antisense inhibition” refers to the production of antisense RNA transcripts capable of suppressing the expression of the target gene or gene product. “Antisense RNA” refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target isolated nucleic acid fragment (U.S. Pat. No. 5,107,065). The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, introns, or the coding sequence.

“Cosuppression” refers to the production of sense RNA transcripts capable of suppressing the expression of the target gene or gene product. “Sense” RNA refers to RNA transcript that includes the mRNA and can be translated into protein within a cell or in vitro. Cosuppression constructs in plants have been previously designed by focusing on overexpression of a nucleic acid sequence having homology to a native mRNA, in the sense orientation, which results in the reduction of all RNA having homology to the overexpressed sequence (see Vaucheret et al., Plant J. 16:651-659 (1998); and Gura, Nature 404:804-808 (2000)). Cosuppression constructs may contain sequences from coding regions or non-coding regions, e.g., introns, 5′-UTRs and 3′-UTRs, or both.

Another variation describes the use of plant viral sequences to direct the suppression of proximal mRNA encoding sequences (PCT Publication No. WO 98/36083 published on Aug. 20, 1998).

RNA interference refers to the process of sequence-specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Fire et al., Nature 391:806 (1998)). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing (PTGS) or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes and is commonly shared by diverse flora and phyla (Fire et al., Trends Genet. 15:358 (1999)).

Small RNAs play an important role in controlling gene expression. Regulation of many developmental processes, including flowering, is controlled by small RNAs. It is now possible to engineer changes in gene expression of plant genes by using transgenic constructs which produce small RNAs in the plant.

Small RNAs appear to function by base-pairing to complementary RNA or DNA target sequences. When bound to RNA, small RNAs trigger either RNA cleavage or translational inhibition of the target sequence. When bound to DNA target sequences, it is thought that small RNAs can mediate DNA methylation of the target sequence. The consequence of these events, regardless of the specific mechanism, is that gene expression is inhibited.

MicroRNAs (miRNAs) are noncoding RNAs of about 19 to about 24 nucleotides (nt) in length that have been identified in both animals and plants (Lagos-Quintana et al., Science 294:853-858 (2001), Lagos-Quintana et al., Curr. Biol. 12:735-739 (2002); Lau et al., Science 294:858-862 (2001); Lee and Ambros, Science 294:862-864 (2001); Llave et al., Plant Cell 14:1605-1619 (2002); Mourelatos et al., Genes. Dev. 16:720-728 (2002); Park et al., Curr. Biol. 12:1484-1495 (2002); Reinhart et al., Genes. Dev. 16:1616-1626 (2002)). They are processed from longer precursor transcripts that range in size from approximately 70 to 200 nt, and these precursor transcripts have the ability to form stable hairpin structures.

MicroRNAs (miRNAs) appear to regulate target genes by binding to complementary sequences located in the transcripts produced by these genes. It seems likely that miRNAs can enter at least two pathways of target gene regulation: (1) translational inhibition; and (2) RNA cleavage. MicroRNAs entering the RNA cleavage pathway are analogous to the 21-25 nt short interfering RNAs (siRNAs) generated during RNA interference (RNAi) in animals and posttranscriptional gene silencing (PTGS) in plants, and likely are incorporated into an RNA-induced silencing complex (RISC) that is similar or identical to that seen for RNAi.

The term “locus” generally refers to a genetically defined region of a chromosome carrying a gene or, possibly, two or more genes so closely linked that genetically they behave as a single locus responsible for a phenotype. When used herein with respect to Fea3, the “Fea3 locus” shall refer to the defined region of the chromosome carrying the Fea3 gene including its associated regulatory sequences.

A “gene” shall refer to a specific genetic coding region within a locus, including its associated regulatory sequences. One of ordinary skill in the art would understand that the associated regulatory sequences will be within a distance of about 4 kb from the Fea3 coding sequence, with the promoter located upstream.

“Germplasm” refers to genetic material of or from an individual (e.g., a plant), a group of individuals (e.g., a plant line, variety or family), or a clone derived from a line, variety, species, or culture. The germplasm can be part of an organism or cell, or can be separate from the organism or cell. In general, germplasm provides genetic material with a specific molecular makeup that provides a physical foundation for some or all of the hereditary qualities of an organism or cell culture. As used herein, germplasm includes cells, seed or tissues from which new plants may be grown, or plant parts, such as leaves, stems, pollen, or cells, that can be cultured into a whole plant.

Sequence alignments and percent identity calculations may be determined using a variety of comparison methods designed to detect homologous sequences including, but not limited to, the Megalign® program of the LASERGENE® bioinformatics computing suite (DNASTAR® Inc., Madison, Wis.). Unless stated otherwise, multiple alignment of the sequences provided herein were performed using the Clustal W method of alignment.

The Clustal W method of alignment (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci. 8:189-191 (1992)) can be found in the MegAlign™ v6.1 program of the LASERGENE® bioinformatics computing suite (DNASTAR® Inc., Madison, Wis.). Default parameters for multiple alignment correspond to GAP PENALTY=10, GAP LENGTH PENALTY=0.2, Delay Divergent Sequences=30%, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB. For pairwise alignments the default parameters are Alignment=Slow-Accurate, Gap Penalty=10.0, Gap Length=0.10, Protein Weight Matrix=Gonnet 250 and DNA Weight Matrix=IUB.

After alignment of the sequences, using the Clustal W program, it is possible to obtain “percent identity” and “divergence” values by viewing the “sequence distances” table on the same program; unless stated otherwise, percent identities and divergences provided and claimed herein were calculated in this manner.

The present invention includes the following isolated polynucleotides and polypeptides:

An isolated polynucleotide comprising: (i) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal W method of alignment, when compared to SEQ ID NO:3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 21, 23, 25 or 27; or (ii) a full complement of the nucleic acid sequence of (i), wherein the full complement and the nucleic acid sequence of (i) consist of the same number of nucleotides and are 100% complementary. Any of the foregoing isolated polynucleotides may be utilized in any recombinant DNA constructs (including suppression DNA constructs) of the present invention. The polypeptide is preferably a FEA3 polypeptide. The polypeptide preferably has FEA3 activity.

An isolated polypeptide having an amino acid sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal W method of alignment, when compared to SEQ ID NO:3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 21, 23, 25 or 27. The polypeptide is preferably a FEA3 polypeptide. The polypeptide preferably has FEA3 activity.

An isolated polynucleotide comprising (i) a nucleic acid sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal W method of alignment, when compared to SEQ ID NO:1, 2, 4, 18, 20, 22, 24 or 26; or (ii) a full complement of the nucleic acid sequence of (i). Any of the foregoing isolated polynucleotides may be utilized in any recombinant DNA constructs (including suppression DNA constructs) of the present invention. The polypeptide is preferably a FEA3 polypeptide. The polypeptide preferably has FEA3 activity.

An isolated polynucleotide comprising a nucleotide sequence, wherein the nucleotide sequence is hybridizable under stringent conditions with a DNA molecule comprising the full complement of SEQ ID NO:1, 2, 4, 18, 20, 22, 24 or 26. The polypeptide is preferably a FEA3 polypeptide. The polypeptide preferably has FEA3 activity.

An isolated polynucleotide comprising a nucleotide sequence, wherein the nucleotide sequence is derived from SEQ ID NO:1, 2, 4, 18, 20, 22, 24 or 26 by alteration of one or more nucleotides by at least one method selected from the group consisting of: deletion, substitution, addition and insertion. The polypeptide is preferably a FEA3 polypeptide. The polypeptide preferably has FEA3 activity.

An isolated polynucleotide comprising a nucleotide sequence, wherein the nucleotide sequence corresponds to an allele of SEQ ID NO:1, 2, 4, 18, 20, 22, 24 or 26.

In one embodiment, the present invention includes recombinant DNA constructs (including suppression DNA constructs). The recombinant DNA construct (including suppression DNA constructs) may comprise a polynucleotide of the present invention operably linked, in sense or antisense orientation, to at least one regulatory sequence (e.g., a promoter functional in a plant). The polynucleotide may comprise 100, 200, 300, 400, 500, 600, 700, 800, 900 or 1000 contiguous nucleotides of SEQ ID NO:1, 2, 4, 18, 20, 22, 24 or 26. The polynucleotide may encode a polypeptide of the present invention.

Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter “Sambrook”).

It is well understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions.

Promoters that can be used for this invention include, but are not limited to, shoot apical meristem specific promoters and shoot apical meristem preferred promoters. Maize knotted 1 promoter, and promoters from genes that are known to be expressed in maize SAM can be used for expressing the polynucleotides disclosed in the current invention. Examples of such genes include, but are not limited to Zm phabulosa, terminal ear1, rough sheath2, rolled leaf1, zyb14, narrow sheath (Ohtsu, K. et al (2007) Plant Journal 52, 391-404). Promoters from orthologs of these genes from other species can be also be used for the current invention.

Examples of Arabidopsis promoters from genes with SAM-preferred expression include, but are not limited to, clv3, aintegumenta-like (ail5, ail6, and ail7) and terminal ear like1, clavata1, wus, shootmeristemless, terminal flower1 (Yadav et al (2009) Proc Natl Acad Sci USA. March 24).

PCT Publication Nos. WO 2004/071467 and U.S. Pat. No. 7,129,089 describe the synthesis of multiple promoter/gene/terminator cassette combinations by ligating individual promoters, genes, and transcription terminators together in unique combinations. Generally, a NotI site flanked by the suitable promoter is used to clone the desired gene. NotI sites can be added to a gene of interest using PCR amplification with oligonucleotides designed to introduce NotI sites at the 5′ and 3′ ends of the gene. The resulting PCR product is then digested with NotI and cloned into a suitable promoter/NotI/terminator cassette. Although gene cloning into expression cassettes is often done using the NotI restriction enzyme, one skilled in the art can appreciate that a number of restriction enzymes can be utilized to achieve the desired cassette. Further, one skilled in the art will appreciate that other cloning techniques including, but not limited to, PCR-based or recombination-based techniques can be used to generate suitable expression cassettes.

In addition, WO 2004/071467 and U.S. Pat. No. 7,129,089 describe the further linking together of individual promoter/gene/transcription terminator cassettes in unique combinations and orientations, along with suitable selectable marker cassettes, in order to obtain the desired phenotypic expression. Although this is done mainly using different restriction enzymes sites, one skilled in the art can appreciate that a number of techniques can be utilized to achieve the desired promoter/gene/transcription terminator combination or orientations. In so doing, any combination and orientation of shoot apical meristem-specific promoter/gene/transcription terminator cassettes can be achieved. One skilled in the art can also appreciate that these cassettes can be located on individual DNA fragments or on multiple fragments where co-expression of genes is the outcome of co-transformation of multiple DNA fragments.

The term “root architecture” refers to the arrangement of the different parts that comprise the root. The terms “root architecture”, “root structure”, “root system” or “root system architecture” are used interchangeably herein.

As referred to herein, alterations in “Root lodging”, “root branching” and “root biomass” are examples of alterations in “root architecture”.

In general, the first root of a plant that develops from the embryo is called the primary root. In most dicots, the primary root is called the taproot. This main root grows downward and gives rise to branch (lateral) roots. In monocots the primary root of the plant branches, giving rise to a fibrous root system.

The term “altered root architecture” refers to aspects of alterations of the different parts that make up the root system at different stages of its development compared to a reference or control plant. It is understood that altered root architecture encompasses alterations in one or more measurable parameters, including but not limited to, the diameter, length, number, angle or surface of one or more of the root system parts, including but not limited to, the primary root, lateral or branch root, adventitious root, and root hairs, all of which fall within the scope of this invention. These changes can lead to an overall alteration in the area or volume occupied by the root.

One of ordinary skill in the art is familiar with protocols for determining alteration in plant root architecture. For example, wt and mutant maize plants can be assayed for changes in root architecture at seedling stage, flowering time or maturity.

Alterations in root architecture can be determined by counting the nodal root numbers of the top 3 or 4 nodes of the greenhouse grown plants or the width of the root band.

“Root band” refers to the width of the mat of roots at the bottom of a pot at plant maturity. Other measures of alterations in root architecture include, but are not limited to, the number of lateral roots, average root diameter of nodal roots, average root diameter of lateral roots, number and length of root hairs.

The extent of lateral root branching (e.g. lateral root number, lateral root length) can be determined by sub-sampling a complete root system, imaging with a flat-bed scanner or a digital camera and analyzing with WinRHIZO™ software (Regent Instruments Inc.).

Root lodging is the measure of plants that do not root lodge; plants that lean from the vertical axis at an approximately 30 degree angle or greater would be counted as root lodged.

One can also evaluate alterations in root lodging, root biomass and root branching by the ability of the plant to increase yield in field testing when compared, under the same conditions, to a control or reference plant.

Data taken on root phenotype are subjected to statistical analysis, normally a t-test to compare the transgenic roots with that of non-transgenic sibling plants. One-way ANOVA may also be used in cases where multiple events and/or constructs are involved in the analysis.

One can also evaluate alterations in root lodging, root biomass and root branching by the ability of the plant to maintain substantial yield (for example, at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% yield) in field testing under stress conditions (e.g., nutrient over-abundance or limitation, water over-abundance or limitation, presence of disease), when compared to the yield of a control or reference plant under non-stressed conditions. The wild-type FEA3 or “fasciated ear3” gene encodes a predicted leucine rich repeat receptor-like protein (LRR-RLP) consisting of 506 amino acids. The terms “wild-type FEA3 gene”, “FEA3 wt gene”, “Fea3 gene” and “FEA3 gene” are used interchangeably herein. Arabidopsis contains three FEA3 orthologues At3g25670, At1g 13230, and At1g68780.

LRR-RLPs constitute a large class of LRR-containing proteins (Wang, G. et al (2010) Critical Reviews in Plant Science, 29: 285-299). Structurally, LRR-RLPs can be divided into the following seven distinct domains: a signal peptide, a cysteine-rich domain, the extracellular LRR (eLRR) domain, a variable domain, an acidic domain, a transmembrane domain, and a short cytoplasmic region (Jones and Jones (1997) Adv. Bot. Res. 24:89-167). The LRR-containing C domain is composed of three subdomains with a non-LRR island subdomain (C2) that interrupts eLRR subdomains C1 and C3, although not all RLPs contain a C2 island (Wang, G. et al. (2008) Plant Physiol 147: 503-517).

Our analysis of fea2/fea3 double mutants indicate that fea2 and fea3 act in independent pathways.

Our analysis of td1/fea3 double mutants indicate that td1 and fea3 act in independent pathways.

The term fasciation, from the Latin fascis, meaning bundle, describes variations in plant form resulting from proliferative growth.

Plants with fea3 mutations, wherein the mutation results in a loss of FEA3 function or loss of FEA3 expression are also called “fea3 plants” or “fea3 null plants”. “fea3 null plants” exhibit the “fea3 phenotype” or the “fea3 null phenotype”. fea3 plants develop larger meristems during inflorescence and floral shoot development, and ear inflorescence meristems show severe fasciation, suggesting that fea3 normally acts to limit the growth of these meristems.

Plants with weak fea3 mutations, wherein the mutation results in a partial loss of fea3 function or partial loss of fea3 expression are also called “fea3 plants with weak fea3 phenotype”. “weak fea3 plants” exhibit the “weak fea3 phenotype”. fea3 plants with weak fea3 alleles exhibit similar phenotype as the fea3 null plants, but to a lesser extent. fea3 plants with weak fea3 alleles may also exhibit partial fea3 null phenotype, that is may not exhibit all the fea3 null characteristics. “Weak fea3 alleles” as referred to herein are fea3 variants or variants of SEQ ID NOS: 1, 2 or 4, which confer weak fea3 phenotype on the plant.

Plants with fea3 mutations that exhibit “null fea3 phenotype” or “weak fea3 phenotype” are referred to herein as plants with “mutant fea3 phenotype”.

The term “dominant negative mutation” as used herein refers to a mutation that has an altered gene product that acts antagonistically to the wild-type allele. These mutations usually result in an altered molecular function (often inactive) and are characterized by a “dominant negative” phenotype. A gene variant, a mutated gene or an allele that confers “dominant negative phenotype” would confer a “null” or a “mutated” phenotype on the host cell even in the presence of a wild-type allele.

As used herein, a polypeptide (or polynucleotide) with “FEA3 activity” refers to a polypeptide (or polynucleotide), that when expressed in a “fea3 mutant line” that exhibits the “fea3 mutant phenotype”, is capable of partially or fully rescuing the fea3 mutant phenotype.

The terms “gene shuffling” and “directed evolution” are used interchangeably herein. The method of “gene shuffling” consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of FEA3 nucleic acids or portions thereof having a modified biological activity (Castle et al., (2004) Science 304(5674): 1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).

“TILLING” or “Targeting Induced Local Lesions IN Genomics” refers to a mutagenesis technology useful to generate and/or identify, and to eventually isolate mutagenised variants of a particular nucleic acid with modulated expression and/or activity (McCallum et al., (2000), Plant Physiology 123:439-442; McCallum et al., (2000) Nature Biotechnology 18:455-457; and, Colbert et al., (2001) Plant Physiology 126:480-484).

TILLING combines high density point mutations with rapid sensitive detection of the mutations. Typically, ethylmethanesulfonate (EMS) is used to mutagenize plant seed. EMS alkylates guanine, which typically leads to mispairing. For example, seeds are soaked in an about 10-20 mM solution of EMS for about 10 to 20 hours; the seeds are washed and then sown. The plants of this generation are known as M1. M1 plants are then self-fertilized. Mutations that are present in cells that form the reproductive tissues are inherited by the next generation (M2). Typically, M2 plants are screened for mutation in the desired gene and/or for specific phenotypes.

TILLING also allows selection of plants carrying mutant variants. These mutant variants may exhibit modified expression, either in strength or in location or in timing (if the mutations affect the promoter for example). These mutant variants may even exhibit lower FEA3 activity than that exhibited by the gene in its natural form. TILLING combines high-density mutagenesis with high-throughput screening methods. The steps typically followed in TILLING are: (a) EMS mutagenesis (Redei G P and Koncz C (1992) In Methods in Arabidopsis Research, Koncz C, Chua N H, Schell J, eds. Singapore, World Scientific Publishing Co, pp. 16-82; Feldmann et al., (1994) In Meyerowitz E M, Somerville C R, eds, Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp 137-172; Lightner J and Caspar T (1998) In J Martinez-Zapater, J Salinas, eds, Methods on Molecular Biology, Vol. 82. Humana Press, Totowa, N.J., pp 91-104); (b) DNA preparation and pooling of individuals; (c) PCR amplification of a region of interest; (d) denaturation and annealing to allow formation of heteroduplexes; (e) DHPLC, where the presence of a heteroduplex in a pool is detected as an extra peak in the chromatogram; (f) identification of the mutant individual; and (g) sequencing of the mutant PCR product. Methods for TILLING are well known in the art (U.S. Pat. No. 8,071,840).

Other mutagenic methods can also be employed to introduce mutations in the FEA3 gene. Methods for introducing genetic mutations into plant genes and selecting plants with desired traits are well known. For instance, seeds or other plant material can be treated with a mutagenic chemical substance, according to standard techniques. Such chemical substances include, but are not limited to, the following: diethyl sulfate, ethylene imine, and N-nitroso-N-ethylurea. Alternatively, ionizing radiation from sources such as X-rays or gamma rays can be used.

Other detection methods for detecting mutations in the FEA3 gene can be employed, e.g., capillary electrophoresis (e.g., constant denaturant capillary electrophoresis and single-stranded conformational polymorphism). In another example, heteroduplexes can be detected by using mismatch repair enzymology (e.g., CELI endonuclease from celery). CELI recognizes a mismatch and cleaves exactly at the 3′ side of the mismatch. The precise base position of the mismatch can be determined by cutting with the mismatch repair enzyme followed by, e.g., denaturing gel electrophoresis. See, e.g., Oleykowski et al., (1998) “Mutation detection using a novel plant endonuclease” Nucleic Acid Res. 26:4597-4602; and, Colbert et al., (2001) “High-Throughput Screening for Induced Point Mutations” Plant Physiology 126:480-484.

The plant containing the mutated fea3 gene can be crossed with other plants to introduce the mutation into another plant. This can be done using standard breeding techniques.

Homologous recombination allows introduction in a genome of a selected nucleic acid at a defined selected position. Homologous recombination has been demonstrated in plants. See, e.g., Puchta et al. (1994), Experientia 50: 277-284; Swoboda et al. (1994), EMBO J. 13: 484-489; Offringa et al. (1993), Proc. Natl. Acad. Sci. USA 90: 7346-7350; Kempin et al. (1997) Nature 389:802-803; and, Terada et al., (2002) Nature Biotechnology, 20(10):1030-1034).

Methods for performing homologous recombination in plants have been described not only for model plants (Offringa et al. (1990) EMBO J. October; 9(10):3077-84) but also for crop plants, for example rice (Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S. Nat Biotechnol. 2002; Iida and Terada: Curr Opin Biotechnol. 2004 April; 15(2):1328). The nucleic acid to be targeted (which may be FEA3 nucleic acid or a variant thereof as hereinbefore defined) need not be targeted to the locus of FEA3 gene respectively, but may be introduced in, for example, regions of high expression. The nucleic acid to be targeted may be weak fea3 allele or a dominant negative allele used to replace the endogenous gene or may be introduced in addition to the endogenous gene.

Transposable elements can be categorized into two broad classes based on their mode of transposition. These are designated Class I and Class II; both have applications as mutagens and as delivery vectors. Class I transposable elements transpose by an RNA intermediate and use reverse transcriptases, i.e., they are retroelements. There are at least three types of Class I transposable elements, e.g., retrotransposons, retroposons, SINE-like elements. Retrotransposons typically contain LTRs, and genes encoding viral coat proteins (gag) and reverse transcriptase, RnaseH, integrase and polymerase (pol) genes. Numerous retrotransposons have been described in plant species. Such retrotransposons mobilize and translocate via a RNA intermediate in a reaction catalyzed by reverse transcriptase and RNase H encoded by the transposon. Examples fall into the Tyl-copia and Ty3-gypsy groups as well as into the SINE-like and LINE-like classifications (Kumar and Bennetzen (1999) Annual Review of Genetics 33:479). In addition, DNA transposable elements such as Ac, TamI and En/Spm are also found in a wide variety of plant species, and can be utilized in the invention. Transposons (and IS elements) are common tools for introducing mutations in plant cells.

The shoot apical meristem (SAM) regulates its size during development by balancing stem cell proliferation and the incorporation of daughter cells into primordia. Several “fasciated” mutants with enlarged meristems have been identified in maize, and can be used to study the genetic basis of meristem size regulation. Two maize genes, thick tassel dwarf1 (td1; Bommert et al. (2005) Development 132:1235-1245) and fasciated ear2 (fea2; Taguchi-Shiobara et al. (2001) Genes Dev. 65 15:2755-2766), are homologous to the Arabidopsis leucine-rich-repeat (LRR) receptor-genes CLAVATA1 (CLV1) and CLAVATA2 (CLV2), respectively. CLV1 and CLV2 were predicted to form a receptor complex that is activated by the CLV3 ligand and represses the stem cell promoting transcription factor WUSCHEL. Analysis of fea2/td1 double mutants however suggested, that the basic CLV1-CLV2 co-receptor model is likely more complex, as the fea2/td1 double mutant showed a more severe phenotype than either single mutant. Recent analysis in Arabidopsis revealed that the separate action of three major receptor complexes (CLV1-BAM1 (BARELY ANY MERISTEM1), CLV2-CRN (CORYNE), and RPK2/TOAD2 (RECEPTOR-LIKE PROTEIN KINASE2/TOADTOOL2)) is necessary for proper meristem size control in Arabidopsis.

Here we present a phenotypic and molecular characterization of the maize mutant fea3 that causes the over-proliferation of the inflorescence meristem, leading to enlarged or fasciated meristems. We cloned the fea3 gene using a map-based cloning approach and the mutant results from an insertion of a partial retrotransposon into an exon of the fea3 locus. We confirmed this identity by isolation of three additional alleles of fea3 derived from a targeted EMS mutagenesis. The FEA3 gene encodes a predicted leucine rich repeat receptor-like protein, related to fea2. In-situ hybridization and Red Fluorescent Protein-tagged transgenic plants show that FEA3 is expressed in the organizing center of SAM and is also expressed in the root apical meristem. FEA3 is localized in the plasma membrane. To determine if FEA3 responds to a CLV3-related (CLE) peptide, we tested its sensitivity to different peptides. The fea3 mutants showed reduced peptide sensitivity, but interestingly they responded to a different CLE peptide compared to FEA2. Double mutants of fea2/fea3 and td1/fea3 have additive and synergistic fasciated phenotypes in ear and tassel, indicating that they act in independent pathways that converge on the same downstream target to control meristem size. Consequently, the function of FEA3 as a receptor protein is in a new pathway distinct from that of TD1 and FEA2.

EMBODIMENTS

In one embodiment, the fea3 variant that can be used in the methods of the current invention is one or more of the following fea3 nucleic acid variants: (i) a portion of a fea3 nucleic acid sequence (SEQ ID NO:1, 2 or 4); (ii) a nucleic acid sequence capable of hybridizing with a fea3 nucleic acid sequence (SEQ ID NO:1, 2 or 4); (iii) a splice variant of a fea3 nucleic acid sequence (SEQ ID NO:1, 2 or 4); (iv) a naturally occurring allelic variant of a fea3 nucleic acid sequence (SEQ ID NO:1, 2 or 4); (v) a fea3 nucleic acid sequence obtained by gene shuffling; (vi) a fea3 nucleic acid sequence obtained by site-directed mutagenesis; (vii) a fea3 variant obtained and identified by the method of TILLING.

In one embodiment, the levels of endogenous FEA3 expression can be decreased in a plant cell by antisense constructs, sense constructs, RNA silencing constructs, RNA interference, artificial microRNAs and genomic disruptions. Examples of genomic disruption include, but are not limited to, disruptions induced by transposons, tilling, homologous recombination.

In one embodiment, a modified plant miRNA precursor may be used, wherein the precursor has been modified to replace the miRNA encoding region with a sequence designed to produce a miRNA directed to FEA3. The precursor is also modified in the star strand sequence to correspond to changes in the miRNA encoding region.

In one embodiment, a nucleic acid variant of FEA3 useful in the methods of the invention is a nucleic acid variant obtained by gene shuffling.

In one embodiment, a genetic modification may also be introduced in the locus of a maize FEA3 gene using the technique of TILLING (Targeted Induced Local Lesions In Genomes).

In one embodiment, site-directed mutagenesis may be used to generate variants of fea3 nucleic acids. Several methods are available to achieve site-directed mutagenesis; the most common being PCR based methods (U.S. Pat. No. 7,956,240).

In one embodiment homologous recombination can also be used to inactivate, or reduce the expression of endogenous FEA3 gene in a plant.

Homologous recombination can be used to induce targeted gene modifications by specifically targeting the FEA3 gene in vivo. Mutations in selected portions of the FEA3 gene sequence (including 5′ upstream, 3′ downstream, and intragenic regions) such as those provided herein are made in vitro and introduced into the desired plant using standard techniques. Homologous recombination between the introduced mutated fea3 gene and the target endogenous FEA3 gene would lead to targeted replacement of the wild-type gene in transgenic plants, resulting in suppression of FEA3 expression or activity.

In one embodiment, catalytic RNA molecules or ribozymes can also be used to inhibit expression of FEA3 gene. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs. A number of classes of ribozymes have been identified. For example, one class of ribozymes is derived from a number of small circular RNAs that are capable of self-cleavage and replication in plants. The RNAs can replicate either alone (viroid RNAs) or with a helper virus (satellite RNAs). Examples of RNAs include RNAs from avocado sunblotch viroid and the satellite RNAs from tobacco ringspot virus, lucerne transient streak virus, velvet tobacco mottle virus, Solanum nodiflorum mottle virus and subterranean clover mottle virus. The design and use of target RNA-specific ribozymes has been described. See, e.g., Haseloff et al. (1988) Nature, 334:585-591.

Another method to inactivate the FEA3 gene is by inhibiting expression is by sense suppression. Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter has been shown to be an effective means by which to block the transcription of a desired target gene. (Napoli et al. (1990), The Plant Cell 2:279-289, and U.S. Pat. Nos. 5,034,323, 5,231,020, and 5,283,184).

In one embodiment, the FEA3 gene can also be inactivated by, e.g., transposon based gene inactivation.

In one embodiment, the inactivating step comprises producing one or more mutations in the FEA3 gene sequence, where the one or more mutations in the FEA3 gene sequence comprise one or more transposon insertions, thereby inactivating the FEA3 gene compared to a corresponding control plant. For example, the mutation may comprise a homozygous disruption in the FEA3 gene or the one or more mutations comprise a heterozygous disruption in the FEA3 gene.

These mobile genetic elements are delivered to cells, e.g., through a sexual cross, transposition is selected for and the resulting insertion mutants are screened, e.g., for a phenotype of interest. Plants comprising disrupted fea3 genes can be crossed with a wt plant. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. The location of a TN (transposon) within a genome of an isolated or recombinant plant can be determined by known methods, e.g., sequencing of flanking regions as described herein. For example, a PCR reaction from the plant can be used to amplify the sequence, which can then be diagnostically sequenced to confirm its origin. Optionally, the insertion mutants are screened for a desired phenotype, such as the inhibition of expression or activity of fea3 or alteration of an agronomic characteristic.

EXAMPLES

The present invention is further illustrated in the following Examples, in which parts and percentages are by weight and degrees are Celsius, unless otherwise stated. It should be understood that these examples, while indicating embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions. Furthermore, various modifications of the invention in addition to those shown and described herein will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.

Example 1 Cloning of Maize Fea3 Gene

A map-based cloning approach was used to isolate the fea3-0 Reference allele (SEQ ID NO:20), which was originally mapped on chromosome 3 (FIG. 1). A partial retrotransposon insertion within a gene encoding a leucine-rich-repeat receptor like protein was identified by fine mapping. To confirm that this insertion was the causative mutation, a targeted EMS screen was performed, which allowed us to identify three additional alleles of fea3, designated fea3-1, -2 and -3 (SEQ ID NOS: 22, 24, and 26 respectively).

fea3 was initially mapped using bulked segregant mapping. A mapping population of 947 individuals was used to place the locus between the BACs c0267MO3 and c0566I18, a region of ˜6 BACs containing ˜25 predicted genes. Sequencing and expression analysis revealed one candidate, an LRR receptor like protein that had a small insertion in the fea3-0 allele. Three additional alleles were identified using a targeted EMS screen from ˜10,000 M1 plants. Sequencing of each allele revealed an amino acid change relative to the progenitor, confirming that the correct gene was isolated.

Example 2 Expression Analysis of FEA2 and FEA3 Genes

RT-PCR was done for FEA2 and FEA3 in different tissues. FIG. 2A shows the expression of FEA22 and FEA3 in different tissues. FEA2 and FEA3 show the strongest expression the shoot apical meristem. FIG. 2B shows the FEA3 expression in situ, showing expression is detected organizing center of meristem. This region overlaps with WUS expression region. This pattern is quite different with other known fasciated ear mutant (Inflorescence transition stage).

Example 3 Maize Mutant Fea3 Phenotype

During vegetative development fea3 mutant plants appear normal. After transition to flowering, however, during early inflorescence development, fea3 mutants ears (FIG. 3B) show a flattened and enlarged inflorescence meristem (IM) compared to wild type (FIG. 3A). At later stages of development enlargement of the IM causes fasciation in the mutant (FIG. 3C). At maturity wild type ears show regularly spaced and organized kernel rows (FIG. 3D), whereas fea3 mutant ears show a progressive enlargement of the ear tip, extra kernel rows and an overall irregular arrangement of rows (FIG. 3E).

Example 4 Fea3/Fea2 Double Mutant Analysis

The tassels of maize fea3/fea2 double mutants are thicker and shorter compared to single mutants (FIG. 4A). Spikelet density was analyzed by counting spikelets per cm along the main rachis. Double mutants show a significant increase in spikelet density, indicating additive effects between fea2 and fea3 (FIG. 4B). Similarly, double mutant ear phenotypes show additive fasciation (FIG. 4C). These results suggest that FEA2 and FEA3 act in different pathways.

Example 5 Clavata3 Peptide Root Assay

In Arabidopsis, CLAVATA2 activity can be detected by responses of root growth to CLAVATA3 (CLV3) peptide. To analyze whether FEA3 and FEA2 respond to CLV3, and determine if they act in a common pathway a CLV3 peptide assay was performed. B73 and homozygous fea2 and fea3 mutant seedlings were germinated and grown on agar plates containing CLV3 peptide. As a control, seedlings were also grown on plates containing a mutated version of the peptide and on plates without any peptide. After 7 days the length of the primary root was measured. B73 wild type plants show strong root growth inhibition as result of response to CLV3 peptide, but fea2 mutants do not respond to CLV3 peptide. Interestingly, fea3 mutants respond to CLV3 peptide, even though FEA3 is expressed in root (FIG. 5).

Example 6 Expression of Red Fluorescent Protein from the FEA3 Promoter

A recombinant DNA construct was made to allow for in vivo localization of FEA3 that has been tagged with Red Fluorescent Protein (RFP). The construct contained the following elements in the 5′ to 3′ orientation: 1) FEA3 Promoter; 2) FEA3 signal peptide coding region; 3) RFP-FEA3 fusion protein coding region; and 4) FEA3 3′-UTR. Transgenic maize plants containing this recombinant DNA construct were produced. Analysis of the transgenic plants revealed that RFP-FEA3 fusion protein was expressed in the inflorescence meristem central zone of both the ear and the tassel.

To see whether FEA3 is localized in the membrane or the soluble fraction, western blot was performed after membrane fractionation. Tissue used was young tassel (about 0.5-3 cm tassel) from the transgenic plant expressing RFP tagged FEA3 protein, as described above. FIG. 2C shows that RFP tagged FEA3 is localized in the plasma membrane, with the arrow indicating band size of about 83 kD which is expected fusion size of RFP tagged FEA3.

Example 7 Clavata3-Like Peptide Root Assay

To analyze whether FEA3 responds to CLV3-like peptides, and determine if they act in a common pathway, a CLV3 peptide assay was performed. The peptides used were ZCL3 (Zea mays CLE-like 3; SEQ ID NO:32), FCP1 (SEQ ID NO:33), CLV3 (SEQ ID NO:34), CLE20 (SEQ ID NO:35), CLE40 (SEQ ID NO:36), ZCL21 (Zea mays CLE-like 3; SEQ ID NO:37), and ZCL23 (Zea mays CLE-like 23; SEQ ID NO:38).

The ZCL peptides were found in maize sequences in the NCBI database by homology search using the CLV3, CLE, and rice related peptides (Fiers et al Plant Cell (2005), 17: 2542-2553; Suzaki et al (2008), Plant Cell, 20: 2049-2058).

B73 and fea3 mutant seedlings were germinated and grown on agar plates containing each 5 μM or 10 μM peptide. As a control, seedlings were also grown on plates containing a scramble of the peptide. After 7 days the length of the primary root was measured. B73 wild type plants show strong root growth inhibition as result of response to ZCL3 (SEQ ID NO:32), FCP1 (SEQ ID NO:33) and CLV3 (SEQ ID NO:34) peptides. Interestingly, fea3 mutants show less sensitivity to FCP1 peptide (FIG. 6).

Example 8 Embryo Culture Assay in Presence of FCP1 Peptide

Wt and fea3 embryos were cultured in the presence of 20 μM FCP1 peptide (SEQ ID NO:33) or 20 μM scrambled peptide. For measurement of embryo SAM growth, about 10 days after pollination, embryos were sterilized (whole corn was sterilized, not individual young seeds) and dissected embryos and put the embryos down on the media and the measurement of SAM size was done two weeks after planting (embryo culture). WT embryo SAM growth was found to be strongly inhibited by FCP1, but fea3 embryos showed resistance (FIG. 7A shows an image comparing wt and fea3 embryo SAM growth, and FIG. 7B shows a quantitative analysis of the same). For the histogram shown in FIG. 7B, p<0.0001

Example 9 Fea3/td1 Double Mutant Analysis

The tassels of maize fea3/td1 double mutants are thicker and shorter compared to single mutants (FIG. 4A). Spikelet density was analyzed by counting spikelets per cm along the main rachis. Double mutants show a significant increase in spikelet density, indicating additive effects between fea2 and fea3 (FIG. 4B). Similarly, double mutant ear phenotypes show additive fasciation (FIG. 4C). These results suggest that FEA2 and FEA3 act in different pathways.

Example 10 Analysis of Fea3 Orthologs in Other Plant Species

Arabidopsis, rice, sorghum and soy orthologs of FEA3 can also be analyzed by doing experiments described in Examples 1-9 for maize FEA3. 

1-26. (canceled)
 27. A modified maize plant comprising an introduced genetic modification in an endogenous fea3 gene encoding a FEA3 polypeptide, wherein the FEA3 polypeptide comprises an amino acid sequence that is at least 95% identical to SEQ ID NO: 3, wherein the modified maize plant exhibits increased kernel row number or kernel number, compared to a control maize plant not comprising the genetic modification.
 28. The maize plant of claim 27, wherein the maize plant exhibits increased grain yield.
 29. The maize plant of claim 27, wherein the maize plant exhibits increased ear size.
 30. The maize plant of claim 27, wherein the genetic modification is a mutation in a coding sequence of the fea3 gene.
 31. The maize plant of claim 27, wherein the genetic modification is a mutation in a non-coding sequence of the fea3 gene.
 32. The maize plant of claim 27, wherein the maize plant exhibits reduced tassels.
 33. A method of identifying an allele of fea3 gene in a maize plant, the method comprising: (a) introducing one or mutations into a fea3 genomic loci encoding a FEA3 polypeptide, the polypeptide comprising an amino acid sequence that is at least 95% identical to SEQ ID NO: 3; (b) growing a population of maize plants comprising the one or more mutations; and (c) identifying a maize plant that exhibits an increase in kernel row number or kernel numbers compared to a control maize plant not comprising the mutation, thereby identifying the fea3 allele.
 34. The method of claim 33, wherein the one or more mutations are introduced in a coding sequence of the fea3 gene.
 35. The method of claim 33, wherein the one or more mutations are introduced in a non-coding sequence of the fea3 gene.
 36. The method of claim 33, wherein the one or more mutations are introduced using a Targeting Induced Local Lesions IN Genomics (TILLING) method.
 37. The method of claim 33, wherein the one or more mutations are selected from the group consisting of deletion, substitution, addition and a combination thereof.
 38. A maize plant produced by the method of claim
 33. 39. A maize seed of the maize plant of claim
 38. 40. A method of identifying a maize plant that has an alteration of at least one agronomic characteristic, the method comprising detecting in the maize plant at least one polymorphism of a marker locus that is associated with said phenotype, wherein the marker locus encodes a polypeptide comprising an amino acid sequence selected from the group consisting of: a) an amino acid sequence having at least 90% identity to SEQ ID NO:3 or 5, wherein expression of said polypeptide in the maize plant results in an alteration of at least one agronomic characteristic selected from the group consisting of: ear meristem size, kernel row number, inflorescence number, branching within the inflorescence, flower number, fruit number, and seed number, when compared to a control plant, wherein the control plant comprises SEQ ID NO:3 or
 5. 41. The method of claim 40, wherein said polypeptide comprises the sequence set forth in SEQ ID NO: 23, 25 or
 27. 